I have 2 furnaces in tandem with the White Rodgers 50A50-207 control. They both ignite and run but randomly one of the furnaces will drop out and give a 1 second flash on the LED. When I reduce the temperature on the thermostat and allow the furnaces to shut down, both will then re-ignite when the temp is brought back up. There is a connection between the boards to keep both blowers running and that seems to work fine. I feel like I am chasing a gremlin because it does not always do this.

Any ideas?

The 1 flash means system lockout. It has tried to start 2 times and failed. What is the make and model number of the furnace?